# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 09:03:28 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 9,9,9-trifluoro-8-oxo-N-phenylnonanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)C(=O)CCCCCCC(=O)Nc1ccccc1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 CF3  CF3  9,9,9-trifluoro-8-oxo-N-phenylnonanamide  ligand  39  21  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CF3
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 CF3  C4    C  CR16  0  -0.319  -6.3071  -1.1546   0.0463
 CF3  C2    C  CR16  0  -0.244  -7.6649  -1.4419  -0.0192
 CF3  C1    C  CR16  0  -0.274  -8.6074  -0.4410  -0.1998
 CF3  C3    C  CR16  0  -0.245  -8.1749   0.8741  -0.3166
 CF3  C5    C  CR16  0  -0.349  -6.8258   1.1767  -0.2534
 CF3  C14   C  CR6   0   0.370  -5.8743   0.1680  -0.0713
 CF3  N1    N  NH1   0  -0.748  -4.5368   0.5704  -0.0145
 CF3  C12   C  C     0   0.558  -3.4088  -0.1792   0.1105
 CF3  O1    O  O     0  -0.469  -3.4091  -1.3955   0.1694
 CF3  C10   C  CH2   0  -0.597  -2.1421   0.6469   0.1920
 CF3  C8    C  CH2   0  -0.412  -0.8711  -0.1690   0.0222
 CF3  C6    C  CH2   0  -0.417   0.3816   0.6886   0.1475
 CF3  C7    C  CH2   0  -0.417   1.6602  -0.1215  -0.0194
 CF3  C9    C  CH2   0  -0.420   2.9194   0.7211   0.1352
 CF3  C11   C  CH2   0  -0.592   4.1747  -0.1182  -0.0407
 CF3  C13   C  C     0   0.219   5.4469   0.6455   0.1377
 CF3  O2    O  O     0  -0.348   5.5363   1.7776   0.5245
 CF3  C15   C  CT    0   0.969   6.7451  -0.1043  -0.2283
 CF3  F3    F  F     0  -0.307   6.8231  -0.2472  -1.5554
 CF3  F1    F  F     0  -0.302   6.7703  -1.3239   0.3131
 CF3  F2    F  F     0  -0.291   7.8216   0.5524   0.1798
 CF3  H4    H  HCR6  0   0.279  -5.6018  -1.9563   0.1863
 CF3  H2    H  HCR6  0   0.257  -7.9821  -2.4728   0.0751
 CF3  H1    H  HCR6  0   0.254  -9.6617  -0.6786  -0.2483
 CF3  H3    H  HCR6  0   0.259  -8.8903   1.6738  -0.4582
 CF3  H5    H  HCR6  0   0.268  -6.5033   2.2075  -0.3476
 CF3  HN1   H  HNH1  0   0.415  -4.3965   1.5682  -0.0718
 CF3  H101  H  HCH2  0   0.276  -2.1370   1.1513   1.1654
 CF3  H102  H  HCH2  0   0.264  -2.1817   1.4477  -0.5529
 CF3  H81   H  HCH2  0   0.224  -0.8769  -0.6636  -0.9535
 CF3  H82   H  HCH2  0   0.225  -0.8389  -0.9644   0.7707
 CF3  H61   H  HCH2  0   0.215   0.3891   1.1830   1.1251
 CF3  H62   H  HCH2  0   0.215   0.3574   1.4899  -0.5988
 CF3  H71   H  HCH2  0   0.217   1.6595  -0.6039  -1.0028
 CF3  H72   H  HCH2  0   0.217   1.6735  -0.9323   0.7171
 CF3  H91   H  HCH2  0   0.233   2.9230   1.1915   1.1216
 CF3  H92   H  HCH2  0   0.234   2.9116   1.5326  -0.5976
 CF3  H111  H  HCH2  0   0.288   4.1858  -0.6020  -1.0237
 CF3  H112  H  HCH2  0   0.296   4.1836  -0.9450   0.6797

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 CF3  C4   C2    aromatic  1.389  0.020  1.389
 CF3  C4   C14   aromatic  1.397  0.020  1.397
 CF3  C4   H4    single    0.930  0.020  1.080
 CF3  C2   C1    aromatic  1.387  0.020  1.387
 CF3  C2   H2    single    0.930  0.020  1.080
 CF3  C1   C3    aromatic  1.389  0.020  1.389
 CF3  C1   H1    single    0.930  0.020  1.080
 CF3  C3   C5    aromatic  1.384  0.020  1.384
 CF3  C3   H3    single    0.930  0.020  1.080
 CF3  C5   C14   aromatic  1.399  0.020  1.399
 CF3  C5   H5    single    0.930  0.020  1.080
 CF3  C14  N1    single    1.398  0.020  1.398
 CF3  N1   C12   single    1.360  0.020  1.360
 CF3  N1   HN1   single    0.860  0.020  1.020
 CF3  C12  O1    double    1.218  0.020  1.218
 CF3  C12  C10   single    1.514  0.020  1.514
 CF3  C10  C8    single    1.520  0.020  1.520
 CF3  C10  H101  single    0.970  0.020  1.090
 CF3  C10  H102  single    0.970  0.020  1.090
 CF3  C8   C6    single    1.523  0.020  1.523
 CF3  C8   H81   single    0.970  0.020  1.090
 CF3  C8   H82   single    0.970  0.020  1.090
 CF3  C6   C7    single    1.523  0.020  1.523
 CF3  C6   H61   single    0.970  0.020  1.090
 CF3  C6   H62   single    0.970  0.020  1.090
 CF3  C7   C9    single    1.523  0.020  1.523
 CF3  C7   H71   single    0.970  0.020  1.090
 CF3  C7   H72   single    0.970  0.020  1.090
 CF3  C9   C11   single    1.520  0.020  1.520
 CF3  C9   H91   single    0.970  0.020  1.090
 CF3  C9   H92   single    0.970  0.020  1.090
 CF3  C11  C13   single    1.495  0.020  1.495
 CF3  C11  H111  single    0.970  0.020  1.090
 CF3  C11  H112  single    0.970  0.020  1.090
 CF3  C13  O2    double    1.200  0.020  1.200
 CF3  C13  C15   single    1.543  0.020  1.543
 CF3  C15  F3    single    1.337  0.020  1.337
 CF3  C15  F1    single    1.335  0.020  1.335
 CF3  C15  F2    single    1.325  0.020  1.325

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 CF3  H4    C4   C14   120.87  3.000
 CF3  H4    C4   C2    119.48  3.000
 CF3  C14   C4   C2    119.65  3.000
 CF3  H2    C2   C1    119.97  3.000
 CF3  H2    C2   C4    118.63  3.000
 CF3  C1    C2   C4    121.41  3.000
 CF3  H1    C1   C3    120.50  3.000
 CF3  H1    C1   C2    120.65  3.000
 CF3  C3    C1   C2    118.86  3.000
 CF3  H3    C3   C5    119.26  3.000
 CF3  H3    C3   C1    120.31  3.000
 CF3  C5    C3   C1    120.43  3.000
 CF3  H5    C5   C14   119.65  3.000
 CF3  H5    C5   C3    119.59  3.000
 CF3  C14   C5   C3    120.76  3.000
 CF3  N1    C14  C5    116.65  3.000
 CF3  N1    C14  C4    124.45  3.000
 CF3  C5    C14  C4    118.89  3.000
 CF3  HN1   N1   C12   115.77  3.000
 CF3  HN1   N1   C14   114.54  3.000
 CF3  C12   N1   C14   129.68  3.000
 CF3  C10   C12  O1    122.85  3.000
 CF3  C10   C12  N1    113.45  3.000
 CF3  O1    C12  N1    123.69  3.000
 CF3  H102  C10  H101  105.53  3.000
 CF3  H102  C10  C8    110.30  3.000
 CF3  H101  C10  C8    110.02  3.000
 CF3  H102  C10  C12   109.41  3.000
 CF3  H101  C10  C12   107.62  3.000
 CF3  C8    C10  C12   113.61  3.000
 CF3  H82   C8   H81   106.39  3.000
 CF3  H82   C8   C6    109.22  3.000
 CF3  H81   C8   C6    109.40  3.000
 CF3  H82   C8   C10   109.81  3.000
 CF3  H81   C8   C10   109.76  3.000
 CF3  C6    C8   C10   112.10  3.000
 CF3  H62   C6   H61   106.14  3.000
 CF3  H62   C6   C7    109.46  3.000
 CF3  H61   C6   C7    109.40  3.000
 CF3  H62   C6   C8    109.73  3.000
 CF3  H61   C6   C8    109.46  3.000
 CF3  C7    C6   C8    112.45  3.000
 CF3  H72   C7   H71   106.12  3.000
 CF3  H72   C7   C9    109.34  3.000
 CF3  H71   C7   C9    109.59  3.000
 CF3  H72   C7   C6    109.29  3.000
 CF3  H71   C7   C6    109.40  3.000
 CF3  C9    C7   C6    112.88  3.000
 CF3  H92   C9   H91   106.58  3.000
 CF3  H92   C9   C11   109.76  3.000
 CF3  H91   C9   C11   109.84  3.000
 CF3  H92   C9   C7    109.68  3.000
 CF3  H91   C9   C7    109.43  3.000
 CF3  C11   C9   C7    111.44  3.000
 CF3  H112  C11  H111  104.85  3.000
 CF3  H112  C11  C13   107.45  3.000
 CF3  H111  C11  C13   108.92  3.000
 CF3  H112  C11  C9    110.30  3.000
 CF3  H111  C11  C9    110.85  3.000
 CF3  C13   C11  C9    114.02  3.000
 CF3  C15   C13  O2    118.19  3.000
 CF3  C15   C13  C11   116.07  3.000
 CF3  O2    C13  C11   125.74  3.000
 CF3  F2    C15  F1    108.21  3.000
 CF3  F2    C15  F3    108.13  3.000
 CF3  F1    C15  F3    107.69  3.000
 CF3  F2    C15  C13   111.68  3.000
 CF3  F1    C15  C13   111.33  3.000
 CF3  F3    C15  C13   109.66  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 CF3  CONST_01  C3   C1   C2   C4      0.00   0.0  0
 CF3  CONST_02  C3   C5   C14  C4      0.00   0.0  0
 CF3  CONST_03  C5   C14  C4   C2      0.00   0.0  0
 CF3  CONST_04  C5   C3   C1   C2      0.00   0.0  0
 CF3  CONST_05  C14  C4   C2   C1      0.00   0.0  0
 CF3  CONST_06  C14  C5   C3   C1      0.00   0.0  0
 CF3  CONST_07  N1   C14  C4   C2    180.00   0.0  0
 CF3  CONST_08  N1   C14  C5   C3    180.00   0.0  0
 CF3  CONST_09  H1   C1   C2   C4    180.00   0.0  0
 CF3  CONST_10  H5   C5   C14  C4    180.00   0.0  0
 CF3  CONST_11  H3   C3   C1   C2    180.00   0.0  0
 CF3  CONST_12  H4   C4   C2   C1    180.00   0.0  0
 CF3  CONST_13  H2   C2   C1   C3    180.00   0.0  0
 CF3  CONST_14  C12  N1   C14  C4      0.00   0.0  0
 CF3  CONST_15  C12  N1   C14  C5    180.00   0.0  0
 CF3  CONST_16  HN1  N1   C14  C4    180.00   0.0  0
 CF3  CONST_17  O1   C12  N1   C14     0.00   0.0  0
 CF3  CONST_18  C10  C12  N1   C14   180.00   0.0  0
 CF3  Var_01    C8   C10  C12  N1   -167.21  30.0  3
 CF3  Var_02    C6   C8   C10  C12  -178.46  30.0  3
 CF3  Var_03    C7   C6   C8   C10   179.92  30.0  3
 CF3  Var_04    C9   C7   C6   C8   -178.71  30.0  3
 CF3  Var_05    C11  C9   C7   C6   -179.86  30.0  3
 CF3  Var_06    C13  C11  C9   C7   -178.37  30.0  3
 CF3  Var_07    O2   C13  C11  C9      7.83  30.0  3
 CF3  Var_08    F3   C15  C13  C11    71.29  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 CF3  plan-1  C4   0.020
 CF3  plan-1  C2   0.020
 CF3  plan-1  C1   0.020
 CF3  plan-1  C3   0.020
 CF3  plan-1  C5   0.020
 CF3  plan-1  C14  0.020
 CF3  plan-1  N1   0.020
 CF3  plan-1  H4   0.020
 CF3  plan-1  H2   0.020
 CF3  plan-1  H1   0.020
 CF3  plan-1  H3   0.020
 CF3  plan-1  H5   0.020
 CF3  plan-2  C14  0.020
 CF3  plan-2  N1   0.020
 CF3  plan-2  C12  0.020
 CF3  plan-2  O1   0.020
 CF3  plan-2  C10  0.020
 CF3  plan-2  HN1  0.020
 CF3  plan-3  C11  0.020
 CF3  plan-3  C13  0.020
 CF3  plan-3  O2   0.020
 CF3  plan-3  C15  0.020

